Flashcards in Exam 3 Deck (82)
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Amino Acids
-Repeating unit of proteins
-Consists of amino group, carboxyl group, hydrogen atom, and variable R group
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Peptide Bonds
-Chemical bond that connects amino acids in a protein
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Polypeptide Chain
-Chain of amino acids linked by peptide bonds
-Protein
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One gene, one polypeptide hypothesis
-Each gene encodes a separate polypeptide chain
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Sense Codons
-Codon that specifies an amino acid in a protein
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Degenerate
-Refers to the fact that the genetic code contains more codons than are needed to specify all 20 AAs
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Synonymous Codons
-Diff codons that specify the same codon
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Isoaccepting tRNAs
-Diff tRNAs w/ diff anticodons that spcify the same AA
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Nonoverlapping
-Each nucleotide is a part of only 1 codon and encodes only 1 AA in a protein
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Reading frame
-Particular way in which a nucleotide sequence is read in groups of 3 nucs (codon) in translation
-Begins w start codon and ends w/ stop codon
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Initiation/ start codon
-Codon that specifies the 1st AA of protein
-fMet in prok, Met in Euk
-Most commonly AUG
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Stop/Termination/Nonsense codons
-Codon in mRNA that signals the end of translation
-UAA, UAG, UGA
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Aminoacyl-tRNA sythetases
-Enzyme that attaches an amino acid to tRNA
-Specific for a particular AA
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tRNA charging
-Chemical rxn in which an aminoacyl-tRNA sythetase attaches an AA to its corresponding tRNA
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IF3
-Protein required for the initiation of translation in proks
-Binds to the small subunit of the ribosome and prevents the large subunit from binding during initiation
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IF1
-Protein required for initiation of translation in proks
-Enhances disociation of the large and small subunits of the ribosome
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IF2
-Protein required for initiation of translation in proks
-Forms a complex w/ GTP and charged tRNA & delivers charged tRNA to initiator complex
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30s initiator complex
-Initial complex formed in the initiation of translayion in proks
-Consists of small subunit of ribosome, mRNA, initiator tRNA charged w fMet, GTP, and IFs 1,2, and 3
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70s initiator complex
-Final complex formed in the initiation of translation in proks
-Small and large ribosomal subunits, mRNA, and intiator tRNA charged w fMet
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Cap binding complex
-A group of proteins in euks
-Binds to 5' cap and initiates translation
-Aids in exporting mRNA from nucleus to cytoplasm
-Promotes initial/pioneer round of translation
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Aminoacyl (A) site
-One of 3 sites in a ribosome occupied by a tRNA during translation
-All charged tRNAs w/ expection of initiator tRNAs first enter the A site
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Peptidyl (P) site
-One of 3 sites in a ribosome occupied by a tRNA during translation
-In elongation stage, tRNAs move from A to P site
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Exit (E) site
-One of 3 sites in a ribosome occupied by a tRNA during translation
-In elongation stage, tRNA moves from P to E site
---Exits the ribosome
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Elongation Factor Tu (EF-Tu)
-Protein taking part in the elongation stage of translation
-Forms a complex w/ GTP and charged tRNA
-Delivers charged tRNA to ribosome
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Elongation Factor Ts (EF-Ts)
-Protein that regenerates EF-Tu in elongation stage of translation
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Translocation
-Movement of a ribosome along mRNA in the course of translation
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Elongation Factor G
-EF-G
-Protein that combines w/ GTP and is required for movement of the ribosome along the mRNA during translation
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Release Factors
-Protein required for termination of translation
-Binds to ribosome when a stop codon is reached and stimulates the release of the polypeptide chain, the tRNA, and the mRNA from the ribsome
-Euk cell requires eRF-1 and eRF-2
-Proks require RF-1, RF-2, and RF-3
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Structural Genes
-DNA sequence that encodes a protein that fxns in metabolism or biosynthesis or that has a structural role in the cell
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Constitutive
-A gene that is expressed continually w/o regulation
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Regulatory elements
-DNA sequence that affects the transcription of other DNA sequences to which it is physically linked
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Domian
-Functional part of protein
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Operon
-Set of structural genes in a prok. cell, along with their common promoter and other sequences (operator) that control their transcription
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Regulator Gene
-Gene associated w an operon in prok cells
-Encode a protein or RNA molecule that fxns in controlling the transcription of one or more structural genes
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Regulator Protein
-Protein produced by a regulator gene
-Binds to another DNA sequence (operator) and controls the transcription of one or more structural genes
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Operator
-DNA sequence in an operon of prok cells
-A regulator protein beings to
-Binding affects rate of transcription of structural genes
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Neg control
-Gene reg in which the binding of a regulator protein to DNA inhibits transcription
-Reg protein= repressor
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Positive control
-Gene reguation in which binding of a reg protein to DNA stimulates transcription
-reg protein= activator
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Inducible operons
-Operon in which transcription is normally turned off so that something must occur for transcription to be induced/turned on
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Repressible Operons
-Operon in which transcription is normally turned on, so that something must happen for transcriotion to be repressed/turned off
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Inducer
-Substance that stimulates transcription in an inducible system of gene regulations
-Usually a molecule that binds to a repressor protein, alters that repressor so that it cannot bind to DNA and inhibit transcription
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Allosteric Proteins
-Protein that changes confirmation upon binding w another molecule
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Corepressor
-Substance that inhibits transcription in a repressible system of gene regulation
-Molecule that binds to a repressor protein and alters it so that the repressor is able to bind to DNA and inhibit transcription
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Coordinate Induction
-The simultaneous synthesis of several enzymes stimulated by a single environmental factor
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Partial Diploid
-Prok cells that possess 2 copies of the same genes
--One on chromosome, one on plasmid
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Catabolite Repression
-System of gene control in prok. operons
-Glucose is used preferentially and the metabolism of other sugas is repressed in the presence of glucose
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Catabolite Activator Protein (CAP)
-Proteins that fxn in catabolite repression
-When bound w cAMP, CAP binds to the promoter of certain operons and stimulates transcription
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cAMP
-Modified nucleotide that fxns in catabolite repression
-Low levels of glucose stimulate high levels of cAMP
---cAMP attaches to CAP, which binds to the promoters of certain operons and stimulates transcription
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Attenuation
-Type of gene regulation in some prok operons
-Transcription is initiated but terminates prematurely b4 transcription of structural genes
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Attenuator
-Secondary structure that forms in the 5' untranslated region of some operons
-Causes the premature termination of transcription
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Antiterminator
-Protein or DNA sequence that inhibits the termination of transcription
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Antisense RNA
-Small RNA mol that bps w a complementary DNA or RNA sequence and affects its fxning
-Control gene expression by binding to sequences on mRNA and inhibiting its translation
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Riboswitches
-Regulatory sequence in an RNA molecule
-When inducer binds to riboswitch, binding changes the configuration of the RNA molecule and alters the expression of RNA
--Usually by affecting the termination of transcription or translation
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Structural Genes on the Lac Operon
-Lac Z--> gene that makes B galactosidase enzyme
-Lac Y--> Permease
---Allows lactose into cell
-Lac A--> Transacetylase
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Lac I
-Regulator gene, encode regulator protein
-Lac I- = nonfunctional repressor protein
-Lac I^s= superrepressor, allolactose cannot bind to it
-Trans
Lac I s> Lac I+ > Lac I-
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Lac O
-operator
-Cis
-LacO^C= Repressor cannot bind to operator region
Lac O c> Lac O+
*Can transcribe structural genes w or w/o lactose
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Lac Operon
-Ex of negative inducible operon
-When lactose levels= high, allolactose converted to lactose by B-galactose, binds to repressor protein
---Repressor cannot bind to operator, transcription occurs
-Lactose levels= low, no allolactose, transcription is inhibited
---Repressor can bind to operator
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DNase I hypersensitivity sites
-Chromatin region that becomes sensitive to digestion by enzyme DNase I
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Chomatin remodeling complexes
-Complex of proteins that alters chromatin structure w/o acetylating histone proteins
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Histone code
-Modifications in histone proteins
-Add. or removal of phosphate, methyl, or acetyl groups that encode info affecting how genes are expressed
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CpG islands
-DNA region that contains many copies of a cytosine base followed by a guanine base
-Often found near transcription start sites in euk DNA
-Cytosine base in CpG commonly methylated when genes are inactive
---Demethylated b4 initiation of transcription
-METHYLATED DNA=REPRESSED TRANSCRIPTION
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3 processes that affect gene regulation by altering chromatin structure
-Chromatin remodeling
-Modification of histone proteins
-DNA methylation
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Methylation of histones
-Histone methyltransferases= add CH3 to histones
-Histone Demethylases= remove CH3
-Activates or represses transcription
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Acetylation of Histones
-Addition stimulates transcription
-CH3CO
-Add by acetyltransferase
-Removed by deacetylases (represses transcription)
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Arabidopsis and Flowering
-FLD stimulates flowering by deacetylating chromatin around FLC
-FLC inhibits flowering, when acetyl groups removed it is inhibited
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Mediators
-Complex of proteins that is one of the components of the basal transcription apparatus
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Insulators
-DNA sequences that blocks or insulates the effect of an enhancer
-Must be located btwn promoter and enhancer to block activity
-May also limit the spread of changes in chromatin structure
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Response Elements
-DNA sequence shared by promoters or enhancers of several euk genes
-Regulatory proteins can bind to stimulate the coordinate transcription of these genes
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Regulation of Galactose Metabolism Through Gal4
-Gal4= transcriptional activator protein
-galactose low= genes not transcribed
---High= genes r transcribed and galactose broken down
-Gal4 binds to UASg--> activates transcription needed to metabolize galactose
-Gal4 and Gal80 bind--> prevents transcription when gal=low
-When galactose= present, Gal3 binds to Gal80 so it cant bind to Gal4--> transcription occurs and galactose is metabolized
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siRNAs scilence transcription by altering chromatin structure
-siRNA combines w protein to create RITS
-Binds to complementary sequence in DNA or RNA molecule in process of being transcribed, repressing transcription by attracting enzymes that methylate histones
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Bacterial Enhancers
-Element that affects transcription but far from gene its affects
-Binding site 4 proteins to increase rate of transcription
--Do this by causing DNA btwn enhancer and promoter to loop out and interact w one another
-Position independent
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Trp Operon
-Ex of neg repressible operon
-5' UTR has 4 complementary regions
---1 comp to 2
---2 comp to 3
---3 comp to 4
-----Allows 5' UTR to make 2 secondary structures
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Attenuation process of Trp Operon
-High levels of tryptophan--> no stalling of ribsome cuz tRNAs are charged
---> Bping of 3 and 4, hairpin followed by Us--> attenuation
-Ribosome partially covers 2 when RNA pol finishes 3, so cannot BP
---3 bps w 4 because it didn't w 2
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Antiterminator process of Trp Operon
-Low levels of tryptophan--> stalling of ribosome cuz tRNA arent charged
---> Bping of 2 and 3, hairpin not followed by Us--> No attenuation
-Ribosome stalls at trp codons UGG
- 2 and 3 bp because ribosome stuck at 1
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Combinatorial Control
-Different combinations of activators and repressors determine transcription
--Stimulates interaction of multiple regulatory proteins (activators and repressors) binding to enhancers and scilencers in diff combos
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3 regions that euk regulatory proteins interact w
1. Core promoter
--Upstream from gene regulating
2. Proximal elements
--Found in reg. promoter, upstream of gene
3. Enhancers and Scilencers
--Proximity-dependent, bind to activators or repressors
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SWI/SNF complex
-Chromatin remodeling
-Uses energy from hydrolysis of ATP
-Slides or ejects nucleosomes, freeing promoters to bind to transcription factors and RNA pol 4 transcription
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What does RNA pol do when it encounters nucleosomes? How does this differ for genes of diff transcription levels?
-Highly transcribed genes--> RNA pol ejects histones, nucleosomes reform on DNA behind RNA pol II
-Lowly transcribed genes--> H2A/H2B dimer is ejected, RNA pol moves around histone hexamer, nucleosomes reform behind RNA pol II
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RNA interference
-A noncoding RNA targets complementary mRNAs w/in a cell for scilencing or degradation
1. miRNAs--> form small hairpins, mRNA unable to be translated
2.siRNAs--> degrades mRNA
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Dicer
-Endonuclease that cuts the dsRNA into 21-25 bp fragments
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RISC
-RNA-induced scilencing complex
-Degrades 1 strand of RNA
-Binds to target mRNA and..
----Cleaves and degrades
----Inhibits translation
----Attracts methylases and deacetylases, spreading heterochromatin
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